Multiple sequence alignment - TraesCS7B01G146100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G146100 chr7B 100.000 4315 0 0 1 4315 189906231 189901917 0.000000e+00 7969.0
1 TraesCS7B01G146100 chr7D 94.805 4350 137 30 1 4314 211631500 211635796 0.000000e+00 6698.0
2 TraesCS7B01G146100 chr7A 94.551 3560 128 32 1 3539 223521229 223524743 0.000000e+00 5439.0
3 TraesCS7B01G146100 chr7A 90.470 808 23 19 3532 4298 223524939 223525733 0.000000e+00 1016.0
4 TraesCS7B01G146100 chr1A 95.174 373 7 3 1618 1988 508205541 508205178 2.890000e-161 579.0
5 TraesCS7B01G146100 chr1A 94.395 339 16 2 2536 2871 508202803 508202465 6.400000e-143 518.0
6 TraesCS7B01G146100 chr1A 95.620 137 5 1 2187 2323 508203963 508203828 7.270000e-53 219.0
7 TraesCS7B01G146100 chr6A 94.609 371 7 2 1618 1988 558036735 558037092 2.910000e-156 562.0
8 TraesCS7B01G146100 chr6A 94.395 339 16 2 2536 2871 558039477 558039815 6.400000e-143 518.0
9 TraesCS7B01G146100 chr6A 96.947 131 3 1 2187 2317 558038315 558038444 7.270000e-53 219.0
10 TraesCS7B01G146100 chr6A 95.122 41 2 0 3464 3504 558039812 558039852 1.000000e-06 65.8
11 TraesCS7B01G146100 chr2A 95.280 339 13 2 2536 2871 651804636 651804298 6.350000e-148 534.0
12 TraesCS7B01G146100 chr2A 94.017 351 14 1 1638 1988 651807438 651807095 3.820000e-145 525.0
13 TraesCS7B01G146100 chr2A 95.620 137 5 1 2187 2323 651805877 651805742 7.270000e-53 219.0
14 TraesCS7B01G146100 chr2A 95.122 41 2 0 3464 3504 651804301 651804261 1.000000e-06 65.8
15 TraesCS7B01G146100 chr2B 80.874 183 18 10 13 181 555837194 555837373 1.260000e-25 128.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G146100 chr7B 189901917 189906231 4314 True 7969.000000 7969 100.00000 1 4315 1 chr7B.!!$R1 4314
1 TraesCS7B01G146100 chr7D 211631500 211635796 4296 False 6698.000000 6698 94.80500 1 4314 1 chr7D.!!$F1 4313
2 TraesCS7B01G146100 chr7A 223521229 223525733 4504 False 3227.500000 5439 92.51050 1 4298 2 chr7A.!!$F1 4297
3 TraesCS7B01G146100 chr1A 508202465 508205541 3076 True 438.666667 579 95.06300 1618 2871 3 chr1A.!!$R1 1253
4 TraesCS7B01G146100 chr6A 558036735 558039852 3117 False 341.200000 562 95.26825 1618 3504 4 chr6A.!!$F1 1886
5 TraesCS7B01G146100 chr2A 651804261 651807438 3177 True 335.950000 534 95.00975 1638 3504 4 chr2A.!!$R1 1866

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
352 353 0.179034 GTAGGGGCTGGATTGCTCTG 60.179 60.0 0.00 0.0 33.17 3.35 F
1037 1054 0.903454 ACCCCACGTACTCCCAAGAG 60.903 60.0 0.00 0.0 46.36 2.85 F
2017 2041 0.666577 CAACGACCAGGAACGAGGAC 60.667 60.0 15.32 0.0 32.83 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2041 0.320771 CCTTGGTGGACGACTCCTTG 60.321 60.000 0.00 0.00 37.48 3.61 R
2970 4921 1.223211 GCTCCTCCTTGAAGGCTCC 59.777 63.158 6.30 0.00 36.29 4.70 R
3408 5364 0.168128 CCGAAACGCTAGCAAAAGGG 59.832 55.000 16.45 6.13 35.65 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 7.040686 ACAATATTTATGTTCGGCCTATGGTTC 60.041 37.037 0.00 0.00 0.00 3.62
108 109 5.550232 TGTGTGCACTAACATTGATGATC 57.450 39.130 19.41 0.00 31.49 2.92
134 135 5.855925 ACGTGCATGTGTTTGTATGTATTTG 59.144 36.000 11.65 0.00 30.89 2.32
187 188 1.471287 GTGTTTATTTGAGGGCCGACC 59.529 52.381 0.00 0.00 40.67 4.79
265 266 5.290493 TGACCTAGATCACTTGTGTTGTT 57.710 39.130 0.00 0.00 0.00 2.83
271 272 9.959721 ACCTAGATCACTTGTGTTGTTTATATT 57.040 29.630 0.00 0.00 0.00 1.28
291 292 3.394674 TCTTTGTAAGTCACCGCATGA 57.605 42.857 0.00 0.00 33.79 3.07
352 353 0.179034 GTAGGGGCTGGATTGCTCTG 60.179 60.000 0.00 0.00 33.17 3.35
407 408 3.898123 TGAAAATCGGAAACATCCCCAAA 59.102 39.130 0.00 0.00 0.00 3.28
413 414 6.806668 ATCGGAAACATCCCCAAATATTTT 57.193 33.333 0.00 0.00 0.00 1.82
445 446 2.263077 GACTGTAAGCAGACACCATCG 58.737 52.381 1.30 0.00 45.28 3.84
578 580 0.988678 AGGAGTAGCCAATCACCCCC 60.989 60.000 0.00 0.00 40.02 5.40
595 597 1.079543 CCGACCACTCCAGCAGAAG 60.080 63.158 0.00 0.00 0.00 2.85
608 611 4.824537 TCCAGCAGAAGAGCATACTAGTAG 59.175 45.833 8.85 0.00 36.85 2.57
609 612 4.582656 CCAGCAGAAGAGCATACTAGTAGT 59.417 45.833 8.85 8.14 36.85 2.73
610 613 5.765677 CCAGCAGAAGAGCATACTAGTAGTA 59.234 44.000 12.38 12.38 34.82 1.82
611 614 6.293735 CCAGCAGAAGAGCATACTAGTAGTAC 60.294 46.154 12.25 1.29 32.84 2.73
612 615 6.485313 CAGCAGAAGAGCATACTAGTAGTACT 59.515 42.308 12.25 8.14 32.84 2.73
613 616 7.658167 CAGCAGAAGAGCATACTAGTAGTACTA 59.342 40.741 12.25 9.66 32.84 1.82
614 617 7.658575 AGCAGAAGAGCATACTAGTAGTACTAC 59.341 40.741 23.03 23.03 32.84 2.73
742 747 3.119096 GTCGCCCCGAGCAAAGAC 61.119 66.667 0.00 0.00 44.04 3.01
777 789 3.971702 AGCCAAGCCCACCTCACC 61.972 66.667 0.00 0.00 0.00 4.02
779 791 3.579302 CCAAGCCCACCTCACCCA 61.579 66.667 0.00 0.00 0.00 4.51
780 792 2.765969 CAAGCCCACCTCACCCAT 59.234 61.111 0.00 0.00 0.00 4.00
781 793 1.379044 CAAGCCCACCTCACCCATC 60.379 63.158 0.00 0.00 0.00 3.51
782 794 2.616458 AAGCCCACCTCACCCATCC 61.616 63.158 0.00 0.00 0.00 3.51
783 795 4.489771 GCCCACCTCACCCATCCG 62.490 72.222 0.00 0.00 0.00 4.18
784 796 3.797353 CCCACCTCACCCATCCGG 61.797 72.222 0.00 0.00 37.81 5.14
875 890 2.367894 CCCCGAATAACCTAGAACCTCC 59.632 54.545 0.00 0.00 0.00 4.30
964 979 1.996748 CCCCGGCCTAAACCCAGTA 60.997 63.158 0.00 0.00 0.00 2.74
1009 1026 1.007842 GTCCTCTTCTCCCCCTCTTCT 59.992 57.143 0.00 0.00 0.00 2.85
1037 1054 0.903454 ACCCCACGTACTCCCAAGAG 60.903 60.000 0.00 0.00 46.36 2.85
1102 1124 1.993370 GCAGATACGAGTTCTTGCGTT 59.007 47.619 0.00 0.00 41.49 4.84
1103 1125 2.028165 GCAGATACGAGTTCTTGCGTTC 59.972 50.000 0.00 0.00 41.49 3.95
1381 1403 1.152860 CTCCGAGCTCTCCCTGCTA 60.153 63.158 12.85 0.00 41.30 3.49
1528 1550 3.483869 GGGATTGGGAGGCTCGCT 61.484 66.667 28.62 12.63 0.00 4.93
2017 2041 0.666577 CAACGACCAGGAACGAGGAC 60.667 60.000 15.32 0.00 32.83 3.85
2429 3837 1.083706 AATGGCTCCCTCCACTCCT 59.916 57.895 0.00 0.00 39.25 3.69
3149 5100 1.880819 GCCTCGACCGGGTGAACTAA 61.881 60.000 3.30 0.00 0.00 2.24
3162 5113 1.483004 TGAACTAATCCGGCGATCCAA 59.517 47.619 9.30 0.00 0.00 3.53
3183 5134 3.696045 ACATCAATCATTCCGGGAAACA 58.304 40.909 14.45 3.43 0.00 2.83
3209 5160 2.957060 TGACCCGTCATTCTCGTCT 58.043 52.632 0.00 0.00 34.14 4.18
3284 5240 6.465948 TGCCAACGTTATTAGGTTTAGAGAA 58.534 36.000 0.00 0.00 30.38 2.87
3307 5263 3.305608 GGTGAAGAAACCAGCCAAGAATG 60.306 47.826 0.00 0.00 40.22 2.67
3335 5291 1.389106 GATGTGCGTTTGGTACTCGTC 59.611 52.381 0.00 0.00 31.78 4.20
3405 5361 5.509716 TCATGATCTGGACAATTTGCATC 57.490 39.130 0.00 0.00 0.00 3.91
3408 5364 1.851304 TCTGGACAATTTGCATCCCC 58.149 50.000 0.88 0.00 0.00 4.81
3469 5431 1.996191 GCACTTTTTGCGGTGAAAACA 59.004 42.857 0.00 0.00 42.79 2.83
3508 5471 0.031616 TGGCTTTCTTGGGGTTTGGT 60.032 50.000 0.00 0.00 0.00 3.67
3714 5916 1.445582 CACGCGGGTAGGTTCAGTC 60.446 63.158 12.47 0.00 0.00 3.51
3718 5920 2.348888 CGGGTAGGTTCAGTCGCCT 61.349 63.158 0.00 0.00 38.81 5.52
3721 5923 1.180029 GGTAGGTTCAGTCGCCTGTA 58.820 55.000 0.00 0.00 39.82 2.74
3746 5967 2.781646 CGGTTTCTTGTTGAAGCGAAAC 59.218 45.455 0.00 0.00 42.57 2.78
3758 5979 1.742880 GCGAAACGGGTTCCCTACC 60.743 63.158 6.31 0.00 46.99 3.18
3835 6057 1.076024 AGTGCAAGATTGGTCATGGGT 59.924 47.619 0.00 0.00 0.00 4.51
3837 6059 0.174162 GCAAGATTGGTCATGGGTGC 59.826 55.000 0.00 0.00 0.00 5.01
3858 6080 1.783071 TCATTGGTGCCATCATGCAT 58.217 45.000 0.00 0.00 44.30 3.96
3952 6174 3.379240 CCTCGCACTGTAATCATCTCTG 58.621 50.000 0.00 0.00 0.00 3.35
4019 6241 7.244886 TGACAAAATATGAAGGTCAGAGAGA 57.755 36.000 0.00 0.00 33.88 3.10
4291 6513 5.733373 GCAGTAAAGTTCTTCACCAACCTTG 60.733 44.000 0.00 0.00 0.00 3.61
4306 6528 2.511659 ACCTTGCTCGCCGTATATCTA 58.488 47.619 0.00 0.00 0.00 1.98
4314 6536 4.143659 GCTCGCCGTATATCTAACGAAAAC 60.144 45.833 0.00 0.00 42.90 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 2.096466 ACATACAAACACATGCACGTCG 60.096 45.455 0.00 0.00 0.00 5.12
134 135 9.696917 AATCACAATCCTTACTTTCAAAACATC 57.303 29.630 0.00 0.00 0.00 3.06
172 173 1.868713 TACAGGTCGGCCCTCAAATA 58.131 50.000 0.08 0.00 43.86 1.40
240 241 5.934625 ACAACACAAGTGATCTAGGTCAATC 59.065 40.000 7.42 0.00 0.00 2.67
265 266 7.766738 TCATGCGGTGACTTACAAAGAATATAA 59.233 33.333 0.00 0.00 0.00 0.98
271 272 3.394674 TCATGCGGTGACTTACAAAGA 57.605 42.857 0.00 0.00 0.00 2.52
291 292 7.378181 ACAGGCAAATCAAACGATCTTTATTT 58.622 30.769 0.00 0.00 0.00 1.40
352 353 0.530870 GGCACTCCGTATTGGCTCTC 60.531 60.000 0.00 0.00 37.80 3.20
445 446 7.415653 GGTCCTGATTGAATTTGATTACTGGTC 60.416 40.741 0.00 0.00 0.00 4.02
578 580 0.108898 CTCTTCTGCTGGAGTGGTCG 60.109 60.000 0.00 0.00 0.00 4.79
620 623 9.656040 CGTTGATATCATACTCCTACTACTAGT 57.344 37.037 6.17 0.00 0.00 2.57
621 624 9.656040 ACGTTGATATCATACTCCTACTACTAG 57.344 37.037 6.17 0.00 0.00 2.57
663 666 9.495572 GGGAAATCTCATGGATTACTAGTTTAG 57.504 37.037 0.00 0.00 43.17 1.85
671 674 5.278660 GCATGTGGGAAATCTCATGGATTAC 60.279 44.000 9.08 5.66 43.17 1.89
742 747 1.858091 CTGGTGGATTCGATCGAAGG 58.142 55.000 31.66 13.70 37.56 3.46
818 833 1.040646 TTCGGGGATGGAGATTCGAG 58.959 55.000 0.00 0.00 0.00 4.04
875 890 1.495584 CCGGTCTGGTGTTTCGTGTG 61.496 60.000 0.00 0.00 0.00 3.82
1009 1026 3.108288 TACGTGGGGTTGCAGCACA 62.108 57.895 4.80 0.00 0.00 4.57
1037 1054 1.181098 ACAACAACAGCCCTGCCATC 61.181 55.000 0.00 0.00 0.00 3.51
1381 1403 2.515057 AGCGTCTCGAGCTCGGAT 60.515 61.111 33.98 15.44 41.83 4.18
1528 1550 0.895530 AATCGAGGCGAGACAAGGAA 59.104 50.000 0.00 0.00 39.91 3.36
1999 2023 1.111116 TGTCCTCGTTCCTGGTCGTT 61.111 55.000 11.89 0.00 0.00 3.85
2017 2041 0.320771 CCTTGGTGGACGACTCCTTG 60.321 60.000 0.00 0.00 37.48 3.61
2164 2702 1.588082 GCTCTTCCCCACGACGTAA 59.412 57.895 0.00 0.00 0.00 3.18
2335 3503 4.444838 CGGGCGACGTTGGGATGA 62.445 66.667 4.64 0.00 37.93 2.92
2429 3837 1.600107 GCACATTACCGTGGAGGGA 59.400 57.895 0.00 0.00 46.96 4.20
2450 3858 5.527582 AGCAGTTAACAAGACAAGATTTCGT 59.472 36.000 8.61 0.00 0.00 3.85
2651 4596 2.542020 TCTTGGACGACTTGATGCAA 57.458 45.000 0.00 0.00 0.00 4.08
2970 4921 1.223211 GCTCCTCCTTGAAGGCTCC 59.777 63.158 6.30 0.00 36.29 4.70
3149 5100 0.180171 TTGATGTTGGATCGCCGGAT 59.820 50.000 5.05 0.00 36.79 4.18
3162 5113 3.696045 TGTTTCCCGGAATGATTGATGT 58.304 40.909 0.73 0.00 0.00 3.06
3183 5134 3.805928 TGACGGGTCATGGCTTCT 58.194 55.556 0.00 0.00 34.14 2.85
3209 5160 2.168521 GGAACTACTGCTGCTGATGGTA 59.831 50.000 13.69 2.50 0.00 3.25
3284 5240 1.494721 TCTTGGCTGGTTTCTTCACCT 59.505 47.619 0.00 0.00 37.75 4.00
3335 5291 3.300009 CGAAGGTTGCAGCTACAAAAAG 58.700 45.455 9.30 0.00 0.00 2.27
3408 5364 0.168128 CCGAAACGCTAGCAAAAGGG 59.832 55.000 16.45 6.13 35.65 3.95
3414 5370 0.672091 TGCATTCCGAAACGCTAGCA 60.672 50.000 16.45 0.00 0.00 3.49
3508 5471 1.696314 GCCTCCCATTCCCCAGGTA 60.696 63.158 0.00 0.00 0.00 3.08
3535 5498 0.611896 GGCCCAAAGGTGTACAGCAT 60.612 55.000 25.75 12.52 34.57 3.79
3683 5871 3.357079 GCGTGTTGCCCCAGTCTG 61.357 66.667 0.00 0.00 37.76 3.51
3714 5916 1.990563 CAAGAAACCGTACTACAGGCG 59.009 52.381 0.00 0.00 0.00 5.52
3718 5920 4.508861 GCTTCAACAAGAAACCGTACTACA 59.491 41.667 0.00 0.00 35.40 2.74
3721 5923 2.542595 CGCTTCAACAAGAAACCGTACT 59.457 45.455 0.00 0.00 35.40 2.73
3758 5979 5.435291 AGAATCTCAGGCTGTCATTAAAGG 58.565 41.667 15.27 0.00 0.00 3.11
3807 6029 1.469703 CCAATCTTGCACTGCGAATGA 59.530 47.619 0.00 0.00 0.00 2.57
3835 6057 1.410882 CATGATGGCACCAATGATGCA 59.589 47.619 0.50 0.00 45.27 3.96
3837 6059 1.410882 TGCATGATGGCACCAATGATG 59.589 47.619 0.00 4.19 39.25 3.07
3858 6080 6.677552 TGATTATGTTTACATTGGATCCCCA 58.322 36.000 9.90 0.00 41.64 4.96
3907 6129 6.077838 GGTCTAAGCAAAACGTTGACATAAG 58.922 40.000 0.00 0.00 36.83 1.73
3952 6174 3.818773 TCCGAAAATCAAGAACTCCAACC 59.181 43.478 0.00 0.00 0.00 3.77
4231 6453 2.115427 TCAGATCACGGGCCAAATAGA 58.885 47.619 4.39 0.00 0.00 1.98
4291 6513 2.888513 TCGTTAGATATACGGCGAGC 57.111 50.000 16.62 0.00 39.38 5.03


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.